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529 add ncbi biosample and project ids to neon soil #354

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mbthornton-lbl
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This PR provides:

A python script to:

  1. generate a changesheet to insert GOLD NcbiBioSampleAccessions and NcbiBioProjectAccessions to Biosample.insdc_biosample_identifiers and OmicsProcessing.insdc_experiment_identifiers.
  2. validate the changes against the metadata/changesheets:validate endpoint.

Note: Validation was performed against the api-napa instance, dev and prod as of Nov 3 blocked by:
#350

Minor updates to simplify setup and some of the methods on the runtime API client.

Output Changefile:
https://drive.google.com/file/d/1bqBgUI8YfQT5ho0Lz02E2mzfCsaBKt-t/view?usp=drive_link

pkalita-lbl
pkalita-lbl previously approved these changes Nov 6, 2023
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@pkalita-lbl pkalita-lbl left a comment

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Overall looks good. Two non-critical comments:

  1. I guess I'm not fully up-to-speed on what the api-napa instance is, but I'm a little confused about the code that sort of uses that term interchangeably with "dev instance". To me "dev" is what's deployed on api-dev.microbiomedata.org. It might make more sense to me to remove the get_runtime_client method and the --use_dev_api flag, and let it all be driven by environment variables. Want to use the api-napa instance? Okay, then set your API_HOST envar accordingly. That's just my outsider view of how I'd expect something like this to work. If that doesn't make sense to you, forget I said anything.
  2. It doesn't look like python-dotenv is listed in main.in but we get it as a transitive dependency of other stuff. If we're using it directly we should list it as a direct dependency.

pkalita-lbl
pkalita-lbl previously approved these changes Nov 14, 2023
@mbthornton-lbl mbthornton-lbl merged commit f1e9caf into main Nov 15, 2023
@mbthornton-lbl mbthornton-lbl deleted the 529_add_NCBI_biosample_and_project_ids_to_NEON_soil branch November 15, 2023 22:48
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2 participants